Code

Exporter, Teiler, QB, DataSHIELD#164

Code

Merged

patrickskowronekdkfz merged 216 commits intomainsamply/bridgehead:mainfrom feature/datashieldsamply/bridgehead:feature/datashieldCopy head branch name to clipboardMar 19, 2024

+788-27

Commits

Commits on Feb 27, 2024

• Add Teiler UI and Teiler module

  djuarezgf

  committed
  2e6edb6

• Add nngm and exliquid modules

  djuarezgf

  committed
  20e2b2a

• Change images of dktk-teiler and dktk-keycloak

  djuarezgf

  committed
  c916a35

• Bugfix: services in teiler-ui-compose.yml

  djuarezgf

  committed
  6340acd

• Configure login extern URLs

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  committed
  eb17d8c

• Rename teiler to exporter

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  committed
  6626f86

• Rename teiler to exporter (bugfix)

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  49be101

• beautiful config

  

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  38c7f3c

• update keykloak config

  

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  c66dac9

• Add original Keycloak config

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  8fe03a6

• Update Teiler Core config

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  efc04ce

• Add Endpoint for Teiler

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  4d1a9bb

• Add Teiler Core

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  17f52a7

• Tidy teiler and mtba volumes

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  c9b1975

• Deactivate traffik for mtba

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  9299a20

• Add forward strategy to teiler-core

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  e2d1095

• Add forward strategy to teiler-core

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  3e0bf38

• Add stripprefix to teiler-core

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  c794508

• Add stripprefix to teiler-ui

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  0a17bbc

• Change volume names for teiler components

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  committed
  4bbd2a1

• Add keycloak teiler app to teiler-ui

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  committed
  3a91259

• Adapt teiler-ui to traefik

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  committed
  fe07c63

• Change salt string for exporter and login

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  committed
  0cfe1d3

• Merge id-management-setup with main

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  32de51e

• Bugfix: cross origins of exporter

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  committed
  72255e6

• Add DataSHIELD

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  0b1e047

• Experiment

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• Add beam connect to docekr-compose

  

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• Experiment

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  68782d1

• beam connect and move beam-connect config

  

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  authored and

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  325ae1d

• Fix beam connect app id

  

  lablans

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  b5ce188

• expose beam connect ports

  

  lablans

  authored and

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  996f53a

• Add Opal Password in Exporter

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  43ab595

• Remove mongo db

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  04cf512

• Remove unnecessary volumes

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  5e376b1

• Add opal certificate

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  687dbba

• ccp.conf in teiler-core as secret

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  e9e1ce5

• Change cert permission and location

  

  Threated

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  f2f4886

• Change beam-connect version and load opal cert

  

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  6438fc5

• change to dockerhub image

  

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• secrets are readonly by default

  

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  276f886

• Switch to no-auth branch of beam-connect

  

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  20c6533

• Add reporter

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  2d7d1d7

• Add parameter LOG_FHIR_VALIDATION to exporter

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  5148e33

• update new broker

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  50360d3

• Migrate to new app key syntax

  

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  c003999

• Add http scheme to exporter

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  36ac8d4

• Generate passwords only if modules are enabled

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  09aa33c

• Remove ports of beam-connect in datashield-compose.yml

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  a1e76a6

• User postgres if docker.verbis.dkfz.de

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  0866cac

• R-Server rock-base:6.3

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  c8bafb2

• Remove unnecessary version of docker-compose.override files

  djuarezgf

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  e182e2f

• Remove todo in rstudio

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  43c45f0

• Enable only if true

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  840096d

• Use LDM_PASSWORD for all admin passwords

  

  lablans

  authored and

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  committed
  73d969e

• Update ccp/modules/datashield-compose.yml

  

  lablans

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  9b8331e

• Update ccp/modules/datashield-compose.yml

  

  lablans

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  4441536

• Generate DATASHIELD_CONNECT_SECRET automatically

  

  lablans

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  committed
  50d28d2

• User default user rstudio in rstudio

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  f3745b9

• Remove IS_DKTK_SITE

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  a6443a6

• Add Teiler Admin to Keycloak

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  committed
  75c86b7

• Add explanation why is the volume of exporter-db currently so important for us.

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  10a362c

• Remove clean temp files configuration of exporter

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  be9adcb

• Remove updater cron of teiler-core

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  c4c4f74

• Add default language to ccp

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  e7f6c0b

• Generate exporter api key automatically

  djuarezgf

  committed
  d97ac56

• Export and QB Curl templates

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  7ed24f6

• Enable Login, Teiler and Exporter

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  2616523

• Add JAVA_OPTS to reporter and exporter

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  bb7451d

• Add DataSHIELD module documentation

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  846e9c2

• Add Exporter module documentation

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  adeaf43

• Add login module documentation

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  e3b8a73

• Add some docs about beam-connect

  

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  b4805af

• Add teiler-ui module documentation

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  957fa64

• Add mtba module documentation

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  c52975f

• Bugfix: JAVA_OPTS for exporter

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  committed
  5d8bec5

• Comment on export and report volumes

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  6cfb42d

• Comment on datashield volume

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  839e7a4

• Remove old comment of exporter-setup.sh

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  973b582

• Fix comment in login-compose.yml

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  f26a8f7

• Comment Keycloak volume

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  4b0b174

• Enable datashield

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  2b61775

• Bugfix: MTBA path prefix

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  765613b

• Disable datashield

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  963144c

• Bugfix: exporter

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  committed
  cfc3c7c

• Bugfix: mtba labels

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  committed
  8d38adc

• Add forward proxy to teiler-core

  djuarezgf

  committed
  ff1f790

• Add site to exporter and reporter

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  committed
  14aece4

• Rename Teiler Backend, Teiler Dashboard and Teiler Orchestrator

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  committed
  2b3eabe

• Bugfix: LDM_AUTH instead of LDM_PASSWORD

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  committed
  7207832

• #!/bin/bash -e

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  ccf0b91

• Bugfix: Add version in every docker compose file

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  4aa8f0f

• Cache opal in /var/cache/bridgehead

  

  lablans

  authored and

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  committed
  862e452

• Autogenerate maps for Opal's beam-connect. To be completed by @Threated with a map-generator in the script.

  

  lablans

  authored and

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  b5ca5ea

• Rework commented sections

  

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  authored and

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  f38d9f8

• Exporter cache

  

  lablans

  authored and

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  c33726d

• Move exporter db to /var/cache/bridgehead

  

  lablans

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  13a74e5

• Rewrite comments

  

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  authored and

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  9cdcf2a

• Add ccp to /var/cache/bridgehead/* volumes

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  7714527

• Auto generate mappings

  

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• Add all sites

  

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  452946a

• Make sure copy works and the correct owner is set

  

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  e2f31b6

• Bugfix: Add version of docker-compose

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  committed
  dcddbf2

• Update ccp/modules/mtba.md

  Show description for 3a6520a
  

  djuarezgf

  and

  lablans

  committed
  3a6520a

• Postgres 15.4 in datashield, exporter and login

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  3dfc4cf

• Bugfix: Exporter and Reporter /var/cache volumes

  djuarezgf

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  c8fc355

• Prevent anonymous volume creation

  

  lablans

  authored and

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  committed
  2237562

• Bugfix: datashield local.json as array

  djuarezgf

  committed
  c1020c5

• Add docu about login in teiler

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  committed
  0039efa

• /var/cache for mtba

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  89c90d3

• Update export template script: FHIR_QUERY to FHIR_PATH

  djuarezgf

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  ec64074

• Use newest version of beam-connect

  

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  058d1c8

• Make Opal use proxy server

  

  lablans

  authored and

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  876c4ef

• Use Bridgehead's internal http proxy

  

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  77240ff

• Prevent creation of volumes

  

  lablans

  authored and

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  committed
  178867c

• Remove nngmSetup in vars

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  committed
  a2c2425

• MTBA 1.0.0

  djuarezgf

  committed
  8d4f487

• Externalize postgres version

  

  lablans

  authored and

  djuarezgf

  committed
  90ee8d6

• Remove unnecessary version of docker-compose.override files

  djuarezgf

  committed
  afb6330

• Remove unnecessary version of docker-compose.override files

  djuarezgf

  committed
  b87d746

• Bugfix: Add version in every docker compose file

  djuarezgf

  committed
  d3edb5e

• Remove unnecessary version of docker-compose.override files

  djuarezgf

  committed
  8e171b7

• Bugfix: Add version in every docker compose file

  djuarezgf

  committed
  3d13695

• Add secret sync to the bridgehead

  

  Threated

  authored and

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  committed
  cec3dfe

• Update to new secret-sync semantics

  

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  f854ab5

• Setup hostname earlier

  

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  4115319

• Make sure path exists

  

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  committed
  93a9132

• Integrate central Keycloak in Teiler

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  committed
  dc3d549

• Generate addtional redirect url

  

  Threated

  authored and

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  committed
  0015365

• Update oidc provider to new url

  

  Threated

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  committed
  3c8ec73

• Add function generate_redirect_urls

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  committed
  bb076c5

• Remove port handeling when generating redirect url

  

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  authored and

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  043e12b

• Account for ip address host values

  

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  131b52f

• Bugfix: Export /var/cache/bridgehead/secrets as environment variables

  djuarezgf

  committed
  9ebbf2e

• Add generate_password function

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  163650f

• Add R-Studio Admin Password

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  8486abe

• Add keycloak configuration

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  e32f484

• Add Keycloak to MTBA

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  committed
  903ef0d

• Add proxy to R-Studio for loading R packages

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  committed
  ae965fd

• Add comment about PASSWORD and DISABLE_AUTH in R-Studio

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  f696585

• Add oauth2_proxy

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  0cd4ede

• Better redirect url handeling

  

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  b44a208

• fix: public client generation

  

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  5d4d040

• Use develop branch for mtba

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  f9b26b6

• mtba latest

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  committed
  25ac4d2

• add /oauth2/callback and /mtba to Keycloak private client

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  committed
  0b2e64a

• mtba develop

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  e411883

• add default template-ids of exporter and reporter

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  committed
  28a612f

• move OAUTH2_SECRET

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  148e873

• fix: Restrict rstudio network access

  

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  0a2dbb4

• feat: Add token-manager to beam

  

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  3710973

• fix: generate the right beam connect mappings

  

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  9f31e95

• fix: Change permissions on new bridgehead dirs

  

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  b73ddc8

• fix: beam connect site renaming

  

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  1edcdce

• fix: chown syntax

  

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  b34f4f2

• fix: opal ssl cert

  

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  d3da426

• fix: only change permissions on related files

  

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  2a024e7

• fix: undo permission changes on startup

  

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  fa141f8

• teiler-orchestrator and teiler-dashboard latest

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  8e5ddc4

• Only users of group DataSHIELD can use R-Studio

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  f6dac70

• Use last version of mtba

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  44d7b34

• Use develop version of mtba

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  0793ea9

• Default values for MTBA

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  37f100d

• Added: Enable MTBA and Enable DataSHIELD to Teiler Backend

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  643e9e6

• Added: allowed-groups

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• Add central token manager beam id

  

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• Add test sites

  

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  2f04e51

• Added: volume for opal metadata db

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  e54475f

• Added: volume for opal metadata db (II)

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  01efc6f

• Added: volume for opal metadata db (III)

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  935c45b

• fix: Generate stable passwords

  

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  f0a05b1

• fix: Use strong pw for opal

  

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• Only sync secrets on startup

  

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  4e3cd68

• Add dsCCPhos

  

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  92a1f4b

• refactor: Use jq from docker

  

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  01d3a38

• fix: Correctly set file permissions

  

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  224c147

• fix: Only give writeable dirs the docker role

  

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  32ffb33

• Use latest jq

  

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  51e8888

• Added: Proxy to R-Studio oauth2-proxy

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  af3e523

• fix: Use forward proxy for secret sync

  

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  4a9427a

• fix: Pull oauth2 proxy from harbor

  

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  b241fee

• fix: secret sync account for minimal override

  

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• refactor: Use beam proxy directly as proxy

  

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  64250d9

• fix: Wait for forward proxy to start

  

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  1995997

• Removed:Login-compose

  djuarezgf

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  97a558d

• Removed: login-compose

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  cea577b

• fix: Start oauth proxy after forward_proxy is ready

  

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  ef8866b

• Integrate central Keycloak in Teiler

  djuarezgf

  committed
  2eb56e6

• Add Keycloak to MTBA

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  committed
  29d2bc0

• Add oauth2_proxy

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  committed
  8a197ce

• Removed: / from groups

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  9a1860c

• Changed: master realm

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  19d0fef

• Changed: replace keycloak with oidc

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  f72e7c7

• chore: Remame datashield mappings to datashield sites

  

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  3e44dab

• chore: Add mannheim to datashield sites

  

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  fb4da54

• fix: Update permissions on update

  

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  74eb86f

• fix: Fix if syntrax

  

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  db96927

Commits on Feb 28, 2024

• Merge pull request #158 from samply/main

  Show description for 7245ddc
  Threated

  authored
  7245ddc

Commits on Mar 11, 2024

• refactor: Move vars to their setup files

  Threated

  committed
  7478d80

Commits on Mar 13, 2024

• Merge pull request #163 from samply/refactor/datashield

  Show description for 1a233b8
  djuarezgf

  authored
  1a233b8

• Merge pull request #145 from samply/feature/datashield-central-keycloak

  Show description for f88dfb5
  djuarezgf

  authored
  f88dfb5

Commits on Mar 14, 2024

• refactor: Move oauth2 proxy related things to datashield setup

  Threated

  committed
  5a6322f

• fix: Dont change ownership of all files under /tmp/bridgehead and /var/cache/bridgehead

  Threated

  committed
  1f17fad

Commits on Mar 18, 2024

• Remove unnecessary comment

  djuarezgf

  committed
  6969a7a

• Remove todo

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  committed
  ff06782

• Rename oauth2_proxy docker service to oauth2-proxy

  djuarezgf

  committed
  349027e

• Remove empty line

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  committed
  591d95e

• Add warning if ENABLE_EXPORTER is not set or set to true

  djuarezgf

  committed
  8cb33c2

• Update lib/functions.sh

  Show description for 3a8df37
  

  djuarezgf

  and

  TKussel

  authored
  3a8df37

• Replace | openssl rsautl -sign with | sha1sum | openssl pkeyutl -sign

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  committed
  3180d0f

• Update minimal/docker-compose.yml

  Show description for d8b9498
  

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  and

  Threated

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• Changed: TEILER_DEFAULT_LANGUAGE

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  committed
  480bbe0

• Remove empty file (teiler-ui-compose.yml)

  djuarezgf

  committed
  adf8e35

Commits on Mar 19, 2024

• Use bridgehead log functions in datashield setup

  TKussel

  committed
  896b24b

• Fix spelling of log WARN

  TKussel

  committed
  ec6f930

• Merge branch 'main' into feature/datashield

  patrickskowronekdkfz

  authored
  4fac079